@@ -14,15 +14,15 @@ Description: Celda is a suite of Bayesian hierarchical models for

     Bayesian method to computationally estimate and remove RNA contamination in

     individual cells without empty droplet information. A variety of scRNA-seq

     data visualization functions is also included.

-Depends: R (>= 4.0)

+Depends: R (>= 4.0), SingleCellExperiment, Matrix

 VignetteBuilder: knitr

 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,

         grDevices, graphics, matrixStats, doParallel, digest, methods,

         reshape2, S4Vectors, data.table,

         Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment,

         MCMCprecision, ggrepel, Rtsne, withr,

-        scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,

-        DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,

+        scater (>= 1.14.4), scran, dbscan,

+        DelayedArray, stringr, ComplexHeatmap, multipanelfigure,

         circlize

 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,

         BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData

@@ -125,6 +125,7 @@ import(grDevices)

 import(graphics)

 import(grid)

 import(uwot)

+importClassesFrom(SingleCellExperiment,SingleCellExperiment)

 importFrom(MCMCprecision,fit_dirichlet)

 importFrom(Matrix,colSums)

 importFrom(Matrix,rowSums)

@@ -144,6 +144,8 @@ setGeneric("decontX", function(x, ...) standardGeneric("decontX"))

 #' @export

 #' @rdname decontX

+#' @importClassesFrom SingleCellExperiment SingleCellExperiment

+#' @importClassesFrom Matrix dgCMatrix

 setMethod("decontX", "SingleCellExperiment", function(x,

                                                       assayName = "counts",

                                                       z = NULL,